Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Dsui_1109 Dsui_1109 ABC-type branched-chain amino acid transport systems, ATPase component
Query= uniprot:Q1MCU2 (292 letters) >FitnessBrowser__PS:Dsui_1109 Length = 266 Score = 197 bits (502), Expect = 2e-55 Identities = 112/263 (42%), Positives = 161/263 (61%), Gaps = 13/263 (4%) Query: 12 DTLLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMI 71 + +L ++++S++FGG+ A+ D SF K +I A+IGPNGAGK+++ N I G Y P G I Sbjct: 13 EVILDLQNISLRFGGVKALTDISFNVKEHEIRAIIGPNGAGKSSMLNVINGVYHPQEGRI 72 Query: 72 TFNQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKASGYT 131 F+ + K+ P T+ +ARTFQNI LF G++VL+N++ + K+ G+ Sbjct: 73 VFHGEERKKME----PHMAATQG--IARTFQNIALFKGMSVLDNIMTGRITKMK--CGFL 124 Query: 132 ILGLIGVGPYKREAA--EAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTG 189 L K E A E +E +LE + P G LPYG Q+R+E+ RA+ Sbjct: 125 EQALYLGRAQKEELAHREKVEEVIDFLEIQHI---RKTPVGRLPYGLQKRVELGRALAAE 181 Query: 190 PELLCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYGQ 249 P LL LDEP AG+N E + + + + GT+I+LIEHDM VVM+ISD +VVL+YG+ Sbjct: 182 PSLLLLDEPMAGMNVEEKQDMCRFILDVNDQFGTTIVLIEHDMGVVMDISDRMVVLDYGK 241 Query: 250 KISDGTPDHVKNDPRVIAAYLGV 272 KI DGTPD V+N+ VI+AYLGV Sbjct: 242 KIGDGTPDDVRNNQEVISAYLGV 264 Lambda K H 0.318 0.136 0.386 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 180 Number of extensions: 10 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 292 Length of database: 266 Length adjustment: 26 Effective length of query: 266 Effective length of database: 240 Effective search space: 63840 Effective search space used: 63840 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory